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Here is a picture of my Model S AutoPilot settings.
I have it set to +5 Km/h ‘Relative Offset’
When I engage AutoPilot where the speed limit is 80 Km/h it will set it to 85 Km/h, where the speed limit is 110 Km/h it will set at 115 Km/h.
You can set the ‘Relative Offset’ a negative amount so if it were set to -1 on your car and the recorded speed limit was 100 Km/h Autopilot would set to 99Km/h but you would be able to adjust it back up to 100.
If you can’t do that your car may be set to 99 Km/h ‘Absolute Offset’ which limits AutoPilot to 99Km/h, which sounds like what is happening in your case.
Please note that this picture is of my Model S and it may be slightly different on your Model 3.
Is the max speed allowable 99Mph? Perhaps the computer is for some reason thinking in miles. Try changing the Mph/Kph setting several times and then back to Kph.
Just a thought.....
if the car percieves the road to not be a dual carriageway it lets you set max 10km/h over. bit annoying if you have single lane highways like we have in australia...